Biology subjects

Ochman, H.

Publications and source records attributed to Ochman, H..

5 recordsLinked to original sources

bioRxiv2026

A multi-omics view of wax synthesis in the wild cochineal bug, Dactylopius opuntiae

This study establishes a comprehensive genomic, transcriptomic, and proteomic foundation for the wild cochineal bug, Dactylopius opuntiae, a scale insect and agricultural pest of prickly pear cacti notable for its dense white waxy covering. Although fatty acyl reductases (FARs) are central to insect epicuticular wax biosynthesis, the genes underlying wax production in cochineal insects are largely unexplored due to a lack of genomic resources. We report a 359-Mb de novo genome assembly in which we identify 26 FAR genes. Through phylogenetic reconstruction of Coccoidea FAR enzymes we reveal lineage-specific expansions of tandemly arranged D. opuntiae FAR genes, and discuss these enzymes roles in the development of this insects epicuticular waxy coating.

molecular biology↗

bioRxiv2025

Recombination and the Species Structure of the Genus Bacteroides

Bacteroides play prominent roles in maintaining gut homeostasis through the fermentation of dietary carbohydrates, the production of metabolites, and the regulation of host immune response. The genus Bacteroides comprises several dozen named species, several of which serve as a nexus of gene exchange in gut microbiomes, especially in humans. Because gene exchange will blur the historically defined species boundaries, we assessed the patterns and extent of recombination for nearly 2,000 fully sequenced Bacteroides genomes representing 36 named species, and redefined species boundaries based on their capacity to exchange genes. We recognized numerous incongruences between traditional classification schemes, those based on nucleotide sequence identity thresholds, and species defined by gene flow. Almost all named species of sufficient sample size for analysis included genomes that failed to recombine with other genomes that were historically assigned to the same species. Such misclassifications occurred even for cases in which sequence identities surpassed the thresholds regularly used to define species. Conversely, we detected instances in which species previously considered distinct were found to recombine extensively--the most striking of which supported unification of B. kribbi, B. koreensis, and B. ovatus (which freely recombines with B. xylanisolvens). Among the broadly distributed populations of B. fragilis, we detected elevated levels of recombination among human-derived strains, although this result is confounded by geographic and sampling biases. Our findings emphasize the utility of a universal species concept based on gene flow, not only for refining bacterial classifications but also for understanding the variation within and across gut microbiomes. IMPORTANCE STATEMENTBacteroides is a diverse genus comprising some of the most pervasive taxa in the mammalian gut microbiome, with several species playing key roles in the maintenance of gut ecosystem stability. The propensity for Bacteroides to exchange genes, both within and among species, has eluded efforts to understand its diversity and to delineate species boundaries, both by traditional classification schemes as well as methods that rely on genomic sequence identity. To circumvent these obstacles and to circumscribe species in a manner that can be uniformly applied across lifeforms, we analyzed all complete genomes assigned to Bacteroides and reclassified them based on their capacity for gene flow, uncovering numerous inconsistencies with both recent and historical classifications. Our approach offers a biologically grounded alternative to the use of sequence identity thresholds, offering a better understanding of the diversity and relationships among genomes within the genus Bacteroides at large.

microbiology↗

bioRxiv2023

Promoter capture drives the emergence of proto-genes in Escherichia coli

The phenomenon of de novo gene birth--the emergence of genes from non-genic sequences--has received considerable attention due to the widespread occurrence of genes that are unique to particular species or genomes. Most instances of de novo gene birth have been recognized through comparative analyses of genome sequences in eukaryotes, despite the abundance of novel, lineage-specific genes in bacteria and the relative ease with which bacteria can be studied in an experimental context. Here, we explore the genetic record of the Escherichia coli Long-Term Evolution Experiment (LTEE) for changes indicative of "proto-genic" phases of new gene birth in which non-genic sequences evolve stable transcription and/or translation. Over the time-span of the LTEE, non-genic regions are frequently transcribed, translated and differentially expressed, thereby serving as raw material for new gene emergence. Most proto-genes result either from insertion element activity or chromosomal translocations that fused pre-existing regulatory sequences to regions that were not expressed in the LTEE ancestor. Additionally, we identified instances of proto-gene emergence in which a previously unexpressed sequence was transcribed after formation of an upstream promoter. Tracing the origin of the causative mutations, we discovered that most occurred early in the history of the LTEE, often within the first 20,000 generations, and became fixed soon after emergence. Our findings show that proto-genes emerge frequently within evolving populations, persist stably, and can serve as potential substrates for new gene formation.

evolutionary biology↗

bioRxiv2023

Origins and Evolution of Novel Bacteroides in Captive Apes

Bacterial strains evolve in response to the gut environment of their hosts, with genomic changes that influence their interactions with hosts as well as with other members of the gut community. Great apes in captivity have acquired strains of Bacteroides xylanisolvens, which are common within gut microbiome of humans but not typically found other apes, thereby enabling characterization of strain evolution following colonization. Here, we isolate, sequence and reconstruct the history of gene gain and loss events in numerous captive-ape-associated strains since their divergence from their closest human-associated strains. We show that multiple captive-ape-associated B. xylanisolvens lineages have independently acquired gene complexes that encode functions related to host mucin metabolism. Our results support the finding of high genome fluidity in Bacteroides, in that several strains, in moving from humans to captive apes, have rapidly gained large genomic regions that augment metabolic properties not previously present in their relatives. Significance statementChronicling the changes that occur in bacterial genomes after a host-switch event is normally difficult due to age of most bacteria-host associations, which renders uncertainties about the bacterial ancestor (and ancestral genome) prior to colonization of the new host. However, the gut microbiomes of great apes in captivity contain bacterial strains that are unique to humans, allowing fine-scale assessment and reconstruction of the genomic changes that follow colonization. By sequencing and comparing closely related strains of Bacteroides that are restricted both to human and to captive great apes, we found that multiple bacterial lineages convergently acquired sets of genes involved in the metabolism of dietary polysaccharides. These results show that over relatively short timescales, the incorporation of strains into microbiomes involves large-scale genomic events that correspond to characteristics of the new host environment.

evolutionary biology↗

bioRxiv2019

Resurrection of a Global, Metagenomically Defined Microvirus

The Gokushovirinae (family Microviridae) are a group of single-stranded, circular DNA bacteriophages that have been detected in metagenomic datasets from every ecosystem on the planet. Despite their abundance, little is known about their biology or their bacterial hosts: isolates are exceedingly rare, known only from a very small number of obligate intracellular bacteria. By synthesizing circularized phage genomes from prophages embedded in diverse enteric bacteria, we produced viable gokushovirus phage particles that could reliably infect E. coli, thereby allowing experimental analysis of its life cycle and growth characteristics. Revived phages integrate into host genomes by hijacking a phylogenetically conserved chromosome-dimer resolution system, in a manner reminiscent of cholera phage CTX. Sequence motifs required for lysogeny are detectable in other metagenomically defined gokushoviruses, but we show that even partial motifs enable phages to persist in a state of pseudolysogeny by continuously producing viral progeny inside hosts without leading to collapse of their host culture. This ability to employ multiple, disparate survival strategies is likely key to the long-term persistence and global distribution of Gokushovirinae. The capacity to harness gokushoviruses as an experimentally tractable model system thus substantially changes our knowledge of the nature and biology of these ubiquitous phages.

microbiology↗